When you install cPanel and WHM on any system, the X interface is disabled. If you are using a machine as a server then you probably shouldn't be running X. There are many reasons for not running X on a server ranging all the way from resource usage to security risks - hence the cPanel/WHM installer disables it.

Fedora Core 6 is not yet supported by cPanel/WHM. To check the status of Fedora Core 6 with regards to cPanel and WHM, check out the following bugzilla report: